A control strategy for fault tolerant PM motors is developed and addresses the operation during a cooling failure in the power-electronic converter. A fault tolerant PM motor interfaced with a parallel H-bridge per-phase topology is considered. Conventional pulse-width modulation (PWM) based voltage generation is used under normal operation. However, the parallel H-bridge module per-phase topology benefits from the capability to generate quasi-square wave (QSW) voltages as an alternative to PWM voltages. The generation of a QSW voltage incurs lower switching losses compared with PWM based voltage generation and the former can be utilized as a safe operating mode for the converter. Typically, converters designed for aero-space applications are equipped with liquid cooling systems and may also require continuous duty operation under cooling system failure. This paper considers the possibility to alternate between these two switching methods for the regulation of converter temperature under contingency e.g., during reduced cooling conditions. Simulated operating point waveforms of current, voltage and torque during PWM and QSW modes are presented for a 18kW 20krpm machine. A reduction in losses in the range of 20%-50% is estimated via simulations. Thermal simulations present the temperature regulation capability with the dual mode controller.